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Items: 1 to 50 of 131

1.

Predicting HLA class II antigen presentation through integrated deep learning.

Chen B, Khodadoust MS, Olsson N, Wagar LE, Fast E, Liu CL, Muftuoglu Y, Sworder BJ, Diehn M, Levy R, Davis MM, Elias JE, Altman RB, Alizadeh AA.

Nat Biotechnol. 2019 Oct 14. doi: 10.1038/s41587-019-0280-2. [Epub ahead of print]

PMID:
31611695
2.

Binding to medium and long chain fatty acyls is a common property of HEAT and ARM repeat modules.

Li TM, Coan JP, Krajewski K, Zhang L, Elias JE, Strahl BD, Gozani O, Chua KF.

Sci Rep. 2019 Oct 2;9(1):14226. doi: 10.1038/s41598-019-50817-6.

3.

Enterovirus pathogenesis requires the host methyltransferase SETD3.

Diep J, Ooi YS, Wilkinson AW, Peters CE, Foy E, Johnson JR, Zengel J, Ding S, Weng KF, Laufman O, Jang G, Xu J, Young T, Verschueren E, Kobluk KJ, Elias JE, Sarnow P, Greenberg HB, Hüttenhain R, Nagamine CM, Andino R, Krogan NJ, Gozani O, Carette JE.

Nat Microbiol. 2019 Sep 16. doi: 10.1038/s41564-019-0551-1. [Epub ahead of print]

PMID:
31527793
4.

Proteomic Discovery of Stool Protein Biomarkers for Distinguishing Pediatric Inflammatory Bowel Disease Flares.

Casavant E, Park KT, Elias JE.

Clin Gastroenterol Hepatol. 2019 Sep 6. pii: S1542-3565(19)30974-7. doi: 10.1016/j.cgh.2019.08.052. [Epub ahead of print]

PMID:
31499250
5.

Latent-period stool proteomic assay of multiple sclerosis model indicates protective capacity of host-expressed protease inhibitors.

Gonzalez CG, Tankou SK, Cox LM, Casavant EP, Weiner HL, Elias JE.

Sci Rep. 2019 Aug 28;9(1):12460. doi: 10.1038/s41598-019-48495-5.

6.

Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin.

Narayan R, Olsson N, Wagar LE, Medeiros BC, Meyer E, Czerwinski D, Khodadoust MS, Zhang L, Schultz L, Davis MM, Elias JE, Levy R.

PLoS One. 2019 Jul 10;14(7):e0219547. doi: 10.1371/journal.pone.0219547. eCollection 2019.

7.

TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets.

Devabhaktuni A, Lin S, Zhang L, Swaminathan K, Gonzalez CG, Olsson N, Pearlman SM, Rawson K, Elias JE.

Nat Biotechnol. 2019 Apr;37(4):469-479. doi: 10.1038/s41587-019-0067-5. Epub 2019 Apr 1.

8.

SETD3 is an actin histidine methyltransferase that prevents primary dystocia.

Wilkinson AW, Diep J, Dai S, Liu S, Ooi YS, Song D, Li TM, Horton JR, Zhang X, Liu C, Trivedi DV, Ruppel KM, Vilches-Moure JG, Casey KM, Mak J, Cowan T, Elias JE, Nagamine CM, Spudich JA, Cheng X, Carette JE, Gozani O.

Nature. 2019 Jan;565(7739):372-376. doi: 10.1038/s41586-018-0821-8. Epub 2018 Dec 10.

9.

Ribosomal protein RPL26 is the principal target of UFMylation.

Walczak CP, Leto DE, Zhang L, Riepe C, Muller RY, DaRosa PA, Ingolia NT, Elias JE, Kopito RR.

Proc Natl Acad Sci U S A. 2019 Jan 22;116(4):1299-1308. doi: 10.1073/pnas.1816202116. Epub 2019 Jan 9.

10.

METTL13 Methylation of eEF1A Increases Translational Output to Promote Tumorigenesis.

Liu S, Hausmann S, Carlson SM, Fuentes ME, Francis JW, Pillai R, Lofgren SM, Hulea L, Tandoc K, Lu J, Li A, Nguyen ND, Caporicci M, Kim MP, Maitra A, Wang H, Wistuba II, Porco JA Jr, Bassik MC, Elias JE, Song J, Topisirovic I, Van Rechem C, Mazur PK, Gozani O.

Cell. 2019 Jan 24;176(3):491-504.e21. doi: 10.1016/j.cell.2018.11.038. Epub 2019 Jan 3.

PMID:
30612740
11.

GPR35 promotes glycolysis, proliferation, and oncogenic signaling by engaging with the sodium potassium pump.

Schneditz G, Elias JE, Pagano E, Zaeem Cader M, Saveljeva S, Long K, Mukhopadhyay S, Arasteh M, Lawley TD, Dougan G, Bassett A, Karlsen TH, Kaser A, Kaneider NC.

Sci Signal. 2019 Jan 1;12(562). pii: eaau9048. doi: 10.1126/scisignal.aau9048.

12.

Genome-wide CRISPR Analysis Identifies Substrate-Specific Conjugation Modules in ER-Associated Degradation.

Leto DE, Morgens DW, Zhang L, Walczak CP, Elias JE, Bassik MC, Kopito RR.

Mol Cell. 2019 Jan 17;73(2):377-389.e11. doi: 10.1016/j.molcel.2018.11.015. Epub 2018 Dec 20.

PMID:
30581143
13.

B-cell lymphomas present immunoglobulin neoantigens.

Khodadoust MS, Olsson N, Chen B, Sworder B, Shree T, Liu CL, Zhang L, Czerwinski DK, Davis MM, Levy R, Elias JE, Alizadeh AA.

Blood. 2019 Feb 21;133(8):878-881. doi: 10.1182/blood-2018-06-845156. Epub 2018 Dec 13. No abstract available.

14.

Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites.

Boucher MJ, Ghosh S, Zhang L, Lal A, Jang SW, Ju A, Zhang S, Wang X, Ralph SA, Zou J, Elias JE, Yeh E.

PLoS Biol. 2018 Sep 13;16(9):e2005895. doi: 10.1371/journal.pbio.2005895. eCollection 2018 Sep.

15.

Developmental phosphoproteomics identifies the kinase CK2 as a driver of Hedgehog signaling and a therapeutic target in medulloblastoma.

Purzner T, Purzner J, Buckstaff T, Cozza G, Gholamin S, Rusert JM, Hartl TA, Sanders J, Conley N, Ge X, Langan M, Ramaswamy V, Ellis L, Litzenburger U, Bolin S, Theruvath J, Nitta R, Qi L, Li XN, Li G, Taylor MD, Wechsler-Reya RJ, Pinna LA, Cho YJ, Fuller MT, Elias JE, Scott MP.

Sci Signal. 2018 Sep 11;11(547). pii: eaau5147. doi: 10.1126/scisignal.aau5147.

16.

Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors.

Pataki CI, Rodrigues J, Zhang L, Qian J, Efron B, Hastie T, Elias JE, Levitt M, Kopito RR.

Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8172-E8180. doi: 10.1073/pnas.1807981115. Epub 2018 Aug 13.

17.

Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota.

Tropini C, Moss EL, Merrill BD, Ng KM, Higginbottom SK, Casavant EP, Gonzalez CG, Fremin B, Bouley DM, Elias JE, Bhatt AS, Huang KC, Sonnenburg JL.

Cell. 2018 Jun 14;173(7):1742-1754.e17. doi: 10.1016/j.cell.2018.05.008.

18.

Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE).

Lill JR, van Veelen PA, Tenzer S, Admon A, Caron E, Elias JE, Heck AJR, Marcilla M, Marino F, Müller M, Peters B, Purcell A, Sette A, Sturm T, Ternette N, Vizcaíno JA, Bassani-Sternberg M.

Proteomics. 2018 Jun;18(12):e1800110. doi: 10.1002/pmic.201800110.

19.

Multiple Click-Selective tRNA Synthetases Expand Mammalian Cell-Specific Proteomics.

Yang AC, du Bois H, Olsson N, Gate D, Lehallier B, Berdnik D, Brewer KD, Bertozzi CR, Elias JE, Wyss-Coray T.

J Am Chem Soc. 2018 Jun 13;140(23):7046-7051. doi: 10.1021/jacs.8b03074. Epub 2018 May 30.

20.

T-Cell Immunopeptidomes Reveal Cell Subtype Surface Markers Derived From Intracellular Proteins.

Olsson N, Schultz LM, Zhang L, Khodadoust MS, Narayan R, Czerwinski DK, Levy R, Elias JE.

Proteomics. 2018 Jun;18(12):e1700410. doi: 10.1002/pmic.201700410. Epub 2018 Apr 18.

21.

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.

Blank C, Easterly C, Gruening B, Johnson J, Kolmeder CA, Kumar P, May D, Mehta S, Mesuere B, Brown Z, Elias JE, Hervey WJ, McGowan T, Muth T, Nunn B, Rudney J, Tanca A, Griffin TJ, Jagtap PD.

Proteomes. 2018 Jan 31;6(1). pii: E7. doi: 10.3390/proteomes6010007.

22.

Liver transplantation in adults with liver disease due to common variable immunodeficiency leads to early recurrent disease and poor outcome.

Azzu V, Elias JE, Duckworth A, Davies S, Brais R, Kumararatne DS, Gimson AES, Griffiths WJH.

Liver Transpl. 2018 Feb;24(2):171-181. doi: 10.1002/lt.24979.

23.

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania.

Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS, Reid G, Knight R, Manjurano A, Changalucha J, Elias JE, Dominguez-Bello MG, Sonnenburg JL.

Science. 2017 Aug 25;357(6353):802-806. doi: 10.1126/science.aan4834.

24.

RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons and is itself regulated by lysine mono-methylation.

Carlson SM, Soulette CM, Yang Z, Elias JE, Brooks AN, Gozani O.

J Biol Chem. 2017 Aug 11;292(32):13381-13390. doi: 10.1074/jbc.M117.784371. Epub 2017 Jun 27.

25.

Characterization of protein complexes of the endoplasmic reticulum-associated degradation E3 ubiquitin ligase Hrd1.

Hwang J, Walczak CP, Shaler TA, Olzmann JA, Zhang L, Elias JE, Kopito RR.

J Biol Chem. 2017 Jun 2;292(22):9104-9116. doi: 10.1074/jbc.M117.785055. Epub 2017 Apr 14.

26.

From mystery to mechanism: can proteomics build systems-level understanding of our gut microbes?

Gonzalez CG, Zhang L, Elias JE.

Expert Rev Proteomics. 2017 Jun;14(6):473-476. doi: 10.1080/14789450.2017.1311211. Epub 2017 Apr 3. No abstract available.

PMID:
28335651
27.

Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens.

Khodadoust MS, Olsson N, Wagar LE, Haabeth OA, Chen B, Swaminathan K, Rawson K, Liu CL, Steiner D, Lund P, Rao S, Zhang L, Marceau C, Stehr H, Newman AM, Czerwinski DK, Carlton VE, Moorhead M, Faham M, Kohrt HE, Carette J, Green MR, Davis MM, Levy R, Elias JE, Alizadeh AA.

Nature. 2017 Mar 30;543(7647):723-727. doi: 10.1038/nature21433. Epub 2017 Mar 22.

28.

Relative Protein Quantification Using Tandem Mass Tag Mass Spectrometry.

Zhang L, Elias JE.

Methods Mol Biol. 2017;1550:185-198. doi: 10.1007/978-1-4939-6747-6_14.

PMID:
28188531
29.

The Prenylated Proteome of Plasmodium falciparum Reveals Pathogen-specific Prenylation Activity and Drug Mechanism-of-action.

Gisselberg JE, Zhang L, Elias JE, Yeh E.

Mol Cell Proteomics. 2017 Apr;16(4 suppl 1):S54-S64. doi: 10.1074/mcp.M116.064550. Epub 2016 Dec 31.

30.

Building proteomic tool boxes to monitor MHC class I and class II peptides.

Schumacher FR, Delamarre L, Jhunjhunwala S, Modrusan Z, Phung QT, Elias JE, Lill JR.

Proteomics. 2017 Jan;17(1-2). doi: 10.1002/pmic.201600061. Review.

PMID:
27928884
31.

Meta-analyses and randomized trials investigating percutaneous coronary intervention of chronic total occlusions: what is left to explore?

Claessen BE, Hoebers LP, Elias JE, van Dongen IM, Henriques JP.

J Thorac Dis. 2016 Sep;8(9):E1100-E1102. No abstract available.

32.

Erratum to: 'Pre-endoscopy point of care test (Simtomax- IgA/IgG-Deamidated Gliadin Peptide) for coeliac disease in iron deficiency anaemia: diagnostic accuracy and a cost saving economic model'.

Lau MS, Mooney PD, White WL, Appleby V, Moreea S, Haythem I, Elias JE, Bundhoo K, Corbett GD, Wong L, Tsai HH, Cross SS, Hebden JM, Hoque S, Sanders DS.

BMC Gastroenterol. 2016 Oct 5;16(1):122. No abstract available.

33.

Isotope-targeted glycoproteomics (IsoTaG) analysis of sialylated N- and O-glycopeptides on an Orbitrap Fusion Tribrid using azido and alkynyl sugars.

Woo CM, Felix A, Zhang L, Elias JE, Bertozzi CR.

Anal Bioanal Chem. 2017 Jan;409(2):579-588. doi: 10.1007/s00216-016-9934-9. Epub 2016 Sep 30.

34.

Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.

Lund PJ, Elias JE, Davis MM.

J Immunol. 2016 Oct 15;197(8):3086-3098. Epub 2016 Sep 21.

35.

A pumpless microfluidic device driven by surface tension for pancreatic islet analysis.

Xing Y, Nourmohammadzadeh M, Elias JE, Chan M, Chen Z, McGarrigle JJ, Oberholzer J, Wang Y.

Biomed Microdevices. 2016 Oct;18(5):80. doi: 10.1007/s10544-016-0109-4.

PMID:
27534648
36.

Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens.

Marceau CD, Puschnik AS, Majzoub K, Ooi YS, Brewer SM, Fuchs G, Swaminathan K, Mata MA, Elias JE, Sarnow P, Carette JE.

Nature. 2016 Jul 7;535(7610):159-63. Epub 2016 Jun 17.

37.

A PWWP Domain of Histone-Lysine N-Methyltransferase NSD2 Binds to Dimethylated Lys-36 of Histone H3 and Regulates NSD2 Function at Chromatin.

Sankaran SM, Wilkinson AW, Elias JE, Gozani O.

J Biol Chem. 2016 Apr 15;291(16):8465-74. doi: 10.1074/jbc.M116.720748. Epub 2016 Feb 24.

38.

Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases.

Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE.

Cell Rep. 2016 Feb 9;14(5):1049-1061. doi: 10.1016/j.celrep.2016.01.009. Epub 2016 Jan 28.

39.

Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets.

Devabhaktuni A, Elias JE.

J Proteome Res. 2016 Mar 4;15(3):732-42. doi: 10.1021/acs.jproteome.5b00861. Epub 2016 Jan 25.

PMID:
26743026
40.

Reproductive Aging Drives Protein Accumulation in the Uterus and Limits Lifespan in C. elegans.

Zimmerman SM, Hinkson IV, Elias JE, Kim SK.

PLoS Genet. 2015 Dec 11;11(12):e1005725. doi: 10.1371/journal.pgen.1005725. eCollection 2015 Dec.

41.

The effect of microbial colonization on the host proteome varies by gastrointestinal location.

Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE.

ISME J. 2016 May;10(5):1170-81. doi: 10.1038/ismej.2015.187. Epub 2015 Nov 17.

42.

Quantitative Imaging of Gut Microbiota Spatial Organization.

Earle KA, Billings G, Sigal M, Lichtman JS, Hansson GC, Elias JE, Amieva MR, Huang KC, Sonnenburg JL.

Cell Host Microbe. 2015 Oct 14;18(4):478-88. doi: 10.1016/j.chom.2015.09.002. Epub 2015 Oct 1.

43.

Metaproteomic analysis adds a functional glimpse into host-microbe succession in an infant's GI.

Elias JE.

Proteomics. 2015 Oct;15(20):3407-8. doi: 10.1002/pmic.201500359.

PMID:
26384154
44.

Monitoring host responses to the gut microbiota.

Lichtman JS, Sonnenburg JL, Elias JE.

ISME J. 2015 Sep;9(9):1908-15. doi: 10.1038/ismej.2015.93. Epub 2015 Jun 9. Review.

45.

A Proteomic Strategy Identifies Lysine Methylation of Splicing Factor snRNP70 by the SETMAR Enzyme.

Carlson SM, Moore KE, Sankaran SM, Reynoird N, Elias JE, Gozani O.

J Biol Chem. 2015 May 8;290(19):12040-7. doi: 10.1074/jbc.M115.641530. Epub 2015 Mar 20.

46.

Idiopathic Non-Cirrhotic Intrahepatic Portal Hypertension (NCIPH)-Newer Insights into Pathogenesis and Emerging Newer Treatment Options.

Goel A, Elias JE, Eapen CE, Ramakrishna B, Elias E.

J Clin Exp Hepatol. 2014 Sep;4(3):247-56. doi: 10.1016/j.jceh.2014.07.005. Epub 2014 Jul 28. Review.

47.

Calcineurin regulates the yeast synaptojanin Inp53/Sjl3 during membrane stress.

Guiney EL, Goldman AR, Elias JE, Cyert MS.

Mol Biol Cell. 2015 Feb 15;26(4):769-85. doi: 10.1091/mbc.E14-05-1019. Epub 2014 Dec 17.

48.

The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis.

Jirawatnotai S, Sharma S, Michowski W, Suktitipat B, Geng Y, Quackenbush J, Elias JE, Gygi SP, Wang YE, Sicinski P.

Cell Cycle. 2014;13(18):2889-900. doi: 10.4161/15384101.2014.946850.

49.

Role of disease-associated tolerance in infectious superspreaders.

Gopinath S, Lichtman JS, Bouley DM, Elias JE, Monack DM.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):15780-5. doi: 10.1073/pnas.1409968111. Epub 2014 Oct 20.

50.

The calcium-dependent protein kinase 3 of toxoplasma influences basal calcium levels and functions beyond egress as revealed by quantitative phosphoproteome analysis.

Treeck M, Sanders JL, Gaji RY, LaFavers KA, Child MA, Arrizabalaga G, Elias JE, Boothroyd JC.

PLoS Pathog. 2014 Jun 19;10(6):e1004197. doi: 10.1371/journal.ppat.1004197. eCollection 2014 Jun.

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